Leak Detection Pump or Hustle? 1999 Stratus

My 1999 Dodge Stratus passed smog on 2-23-05 when it was owned by someone else. After I bought it, it stopped cold, was repaired and both the fuel and water pumps and most of the fuel system was replaced and a recall repair made on the shift, involving drilling of the shift lever dimple and installing a rod. The shift was fine before the recall repair, but is now not operating properly. Immediately the next day after the repair was completed the check engine light went on and the car will not pass smog. The place that repaired the car says it is a faulty leak detection pump (DTC P1494, mechanical fault) and no fault of theirs. In order to confirm this, they want to charge me $100 just to look at it. Someone else who ran computer diagnostics as a favor says it is a leak sensor and I have been able to actually hear the hiss of a leak myself, but only since the repair was made. The repair shop now wants almost $500 to replace the leak detection pump so the car can pass smog. However, I have learned that kinks and the like in the supply vacuum lines can cause misdiagnosis, especially in this vehicle. I am wondering if the repair people are responsible for kinking the lines up or messing up the seals during the repairs to the fuel system, since the lines run all the way from the engine compartment to the fuel tank. Shouldn't they have checked the lines before giving the car back to me? The repair manager is telling me all this is just a coincidence, and he is being far too cagey about it. Here in Sacramento CA we have a lot of hinky things going on with vehicle repairs, and I am very suspicious. I need someone to give me an honest opinion. Thank You